I've got krusader and kdiff3 and when I try to use the 'Compare by content' command, krusader opens kdiff3 and then 'Opening of these files failed' error occurs.When I use kdiff3 separately, it works fine.Does anybody else face this problem?Is there a fix?

Yup, you both do. That may be the cause of your problem. You'll either have to wait for the later version to be built and put in the Entropy repository (no doubt that'll happen within a few days), or build the later version using Portage.